ENST00000579299.2:n.-31T>G

Variant names:

• chr17-30529657-T-G
• rs216465
• ENST00000579299.2:n.-31T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579299.2(ALOX12P1):​n.-31T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,420 control chromosomes in the GnomAD database, including 14,833 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (14807 hom., cov: 32)
  • Exomes 𝑓: 0.38 (26 hom.)
• Consequence: ALOX12P1 ENST00000579299.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 1 publications found

Genes affected

ALOX12P1 (HGNC:431): (arachidonate 12-lipoxygenase pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579299.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALOX12P1	ENST00000579299.2	TSL:6	n.-31T>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65226 AN: 151860 Hom.: 14801 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.450

GnomAD4 exome AF: 0.375 AC: 165 AN: 440 Hom.: 26 Cov.: 0 AF XY: 0.354 AC XY: 95 AN XY: 268

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.383 AC: 163 AN: 426

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.125 AC: 1 AN: 8

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.429 AC: 65247 AN: 151980 Hom.: 14807 Cov.: 32 AF XY: 0.434 AC XY: 32257 AN XY: 74296

African (AFR) AF: 0.337 AC: 13988 AN: 41464

American (AMR) AF: 0.484 AC: 7385 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1639 AN: 3470

East Asian (EAS) AF: 0.837 AC: 4315 AN: 5158

South Asian (SAS) AF: 0.478 AC: 2296 AN: 4802

European-Finnish (FIN) AF: 0.410 AC: 4333 AN: 10564

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29793 AN: 67960

Other (OTH) AF: 0.452 AC: 950 AN: 2102

Alfa AF: 0.425 Hom.: 2300

Bravo AF: 0.434

Asia WGS AF: 0.600 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	9.8
DANN	Benign	0.75
PhyloP100		-0.076

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs216465; hg19: chr17-28856675;